Variant 12-88507004-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_000899.5(KITLG):c.714+24T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,229,410 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 4 hom. )

Consequence

KITLG
NM_000899.5 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.95

Variant links:

Genes affected

KITLG (HGNC:6343): (KIT ligand) This gene encodes the ligand of the tyrosine-kinase receptor encoded by the KIT locus. This ligand is a pleiotropic factor that acts in utero in germ cell and neural cell development, and hematopoiesis, all believed to reflect a role in cell migration. In adults, it functions pleiotropically, while mostly noted for its continued requirement in hematopoiesis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

KITLG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 12-88507004-A-T is Benign according to our data. Variant chr12-88507004-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1201062.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00181 (275/152314) while in subpopulation NFE AF= 0.0017 (116/68036). AF 95% confidence interval is 0.00145. There are 1 homozygotes in gnomad4. There are 151 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KITLG	NM_000899.5 linkuse as main transcript	c.714+24T>A		intron_variant		ENST00000644744.1
KITLG	NM_003994.6 linkuse as main transcript	c.630+24T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KITLG	ENST00000644744.1 linkuse as main transcript	c.714+24T>A		intron_variant			NM_000899.5	P1	P21583-1

Frequencies

GnomAD3 genomes

AF:

0.00181

AC:

275

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000197

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00970

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00170

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00182

AC:

454

AN:

248872

Hom.:

AF XY:

0.00197

AC XY:

266

AN XY:

134856

show subpopulations

Gnomad AFR exome

AF:

0.000887

Gnomad AMR exome

AF:

0.000495

Gnomad ASJ exome

AF:

0.000200

Gnomad EAS exome

AF:

0.000329

Gnomad SAS exome

AF:

0.000132

Gnomad FIN exome

AF:

0.00982

Gnomad NFE exome

AF:

0.00163

Gnomad OTH exome

AF:

0.00264

GnomAD4 exome

AF:

0.00142

AC:

1532

AN:

1077096

Hom.:

Cov.:

AF XY:

0.00141

AC XY:

779

AN XY:

554156

show subpopulations

Gnomad4 AFR exome

AF:

0.000499

Gnomad4 AMR exome

AF:

0.000408

Gnomad4 ASJ exome

AF:

0.000801

Gnomad4 EAS exome

AF:

0.000211

Gnomad4 SAS exome

AF:

0.0000894

Gnomad4 FIN exome

AF:

0.00896

Gnomad4 NFE exome

AF:

0.00123

Gnomad4 OTH exome

AF:

0.00111

GnomAD4 genome

AF:

0.00181

AC:

275

AN:

152314

Hom.:

Cov.:

AF XY:

0.00203

AC XY:

151

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00970

Gnomad4 NFE

AF:

0.00170

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00151

Hom.:

Bravo

AF:

0.000922

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 22, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.0060

DANN

Benign

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over